Sentence examples for permutations were calculated from inspiring English sources

For multiple testing correction of association p-values, permutations were calculated by permuting phenotype labels and performing tests of association as normal; for each raw p-value, we computed the number of permutations for which a p-value equal to, or lower than, the original raw p-value was reached and divide this by the number of permutations, the result of which is the adjusted p-value.

All permutations were calculated for different traits in data sets for crosses and chromosomes separately.

Global and pairwise and heterozygosity standardized, and associated statistical difference from zero based on 9999 permutations were calculated using GENODIVE 2.0b23.

Initial density permutations were calculated for each CpG beacon by counting the number of CpG beacons within a region of 499bp downstream and 500 bp upstream.

Linkage disequilibrium between pairs of microsatellite loci and between pairs of microsatellite loci and populations, using 10,000 permutations, were calculated with GENEPOP version 4.1.4 software (Rousset, 2008).

The number of permutations per transcript was increased until the maximum LOD score from the true data was no longer in the top ten of LOD scores from the permutation, or until 1,000,000 permutations were calculated.

The P-value of the odds ratios obtained by the permutations was calculated from the proportion of permuted datasets that were more extreme than the observations in the real trait-associated SNP set.

The average of the false positive numbers over 100 permutations is calculated as FP.

P value based on 100,000 times permutations was calculated by using PLINK 1.07 software (Massachusetts General Hospital, Boston, MA) [ 35].

In the adaptive approach, permutation test statistics are sampled until either r of these statistics are larger than the observed statistic, or b total permutations are calculated with R total successes, where R <  r.

The exon-level implementation of RP has better sensitivity than that of the gene-level version (data not shown) and is faster since permutations are calculated only once and not gene by gene.